Entering edit mode
3.4 years ago
i.am.filippov
•
0
I was following Seurat tutorial on clustering single-cell ATAC data. Here's the code for loading the data:
input_data <- Read10X_h5(filename = "./data/pbmc_granulocyte_sorted_3k_filtered_feature_bc_matrix.h5")
atac_counts <- input_data$Peaks
metadata <- read.csv(
file = "./data/pbmc_granulocyte_sorted_3k_per_barcode_metrics.csv",
header = TRUE,
row.names = 1
)
chrom_assay <- CreateChromatinAssay(
counts = atac_counts,
sep = c(":", "-"),
genome = 'hg38',
fragments = './data/pbmc_granulocyte_sorted_3k_atac_fragments.tsv.gz',
min.cells = 10,
min.features = 200
)
pbmc <- CreateSeuratObject(
counts = chrom_assay,
assay = "peaks",
meta.data = metadata
)
Some filtering code...and then:
pbmc <- RunUMAP(object = pbmc, reduction = 'lsi', dims = 2:30)
pbmc <- FindNeighbors(object = pbmc, reduction = 'lsi', dims = 2:30)
pbmc <- FindClusters(object = pbmc, verbose = FALSE, algorithm = 3)
DimPlot(object = pbmc, label = TRUE) + NoLegend()
I can see the clusters on UMAP plot, so they're there. However, I can't see the clusters in metadata:
colnames(pbmc@meta.data)
[1] "orig.ident" "nCount_peaks" "nFeature_peaks"
[4] "gex_barcode" "atac_barcode" "is_cell"
[7] "excluded_reason" "gex_raw_reads" "gex_mapped_reads"
[10] "gex_conf_intergenic_reads" "gex_conf_exonic_reads" "gex_conf_intronic_reads"
[13] "gex_conf_exonic_unique_reads" "gex_conf_exonic_antisense_reads" "gex_conf_exonic_dup_reads"
[16] "gex_exonic_umis" "gex_conf_intronic_unique_reads" "gex_conf_intronic_antisense_reads"
[19] "gex_conf_intronic_dup_reads" "gex_intronic_umis" "gex_conf_txomic_unique_reads"
[22] "gex_umis_count" "gex_genes_count" "atac_raw_reads"
[25] "atac_unmapped_reads" "atac_lowmapq" "atac_dup_reads"
[28] "atac_chimeric_reads" "atac_mitochondrial_reads" "atac_fragments"
[31] "atac_TSS_fragments" "atac_peak_region_fragments" "atac_peak_region_cutsites"
[34] "nucleosome_signal" "nucleosome_percentile" "TSS.enrichment"
[37] "TSS.percentile" "pct_reads_in_peaks" "high.tss"
Thanks in advance!